Open Access Software

Brunn: An open source laboratory information system for microplates with a graphical plate layout design process

Jonathan Alvarsson1*, Claes Andersson2, Ola Spjuth1, Rolf Larsson2 and Jarl ES Wikberg1

Author Affiliations

1 Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden

2 Department of Medical Sciences, Uppsala University, Uppsala University Hospital, Uppsala, Sweden

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BMC Bioinformatics 2011, 12:179  doi:10.1186/1471-2105-12-179

Published: 20 May 2011



Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expensive, and heavyweight and there is a need for a flexible lightweight open system for handling plate design, and validation and preparation of data.


A Bioclipse plugin consisting of a client part and a relational database was constructed. A multiple-step plate layout point-and-click interface was implemented inside Bioclipse. The system contains a data validation step, where outliers can be removed, and finally a plate report with all relevant calculated data, including dose-response curves.


Brunn is capable of handling the data from microplate assays. It can create dose-response curves and calculate IC50 values. Using a system of this sort facilitates work in the laboratory. Being able to reuse already constructed plates and plate layouts by starting out from an earlier step in the plate layout design process saves time and cuts down on error sources.